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152  structures 2839  species 7  interactions 4727  sequences 91  architectures

Family: Ribonuc_red_lgC (PF02867)

Summary: Ribonucleotide reductase, barrel domain

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Ribonucleotide reductase, barrel domain Provide feedback

No Pfam abstract.

Literature references

  1. Uhlin U, Eklund H; , Nature 1994;370:533-539.: Structure of ribonucleotide reductase protein R1. PUBMED:8052308 EPMC:8052308


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000788

Ribonucleotide reductase (EC) [PUBMED:3286319, PUBMED:8511586] catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs divide into three classes on the basis of their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, bacteriophage and viruses, use a diiron-tyrosyl radical, Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in anaerobic bacteria and bacteriophage, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes.

Ribonucleotide reductase is an oligomeric enzyme composed of a large subunit (700 to 1000 residues) and a small subunit (300 to 400 residues) - class II RNRs are less complex, using the small molecule B12 in place of the small chain [PUBMED:11875520].

The reduction of ribonucleotides to deoxyribonucleotides involves the transfer of free radicals, the function of each metallocofactor is to generate an active site thiyl radical. This thiyl radical then initiates the nucleotide reduction process by hydrogen atom abstraction from the ribonucleotide [PUBMED:9309223]. The radical-based reaction involves five cysteines: two of these are located at adjacent anti-parallel strands in a new type of ten-stranded alpha/beta-barrel; two others reside at the carboxyl end in a flexible arm; and the fifth, in a loop in the centre of the barrel, is positioned to initiate the radical reaction [PUBMED:8052308]. There are several regions of similarity in the sequence of the large chain of prokaryotes, eukaryotes and viruses spread across 3 domains: an N-terminal domain common to the mammalian and bacterial enzymes; a C-terminal domain common to the mammalian and viral ribonucleotide reductases; and a central domain common to all three [PUBMED:9309223].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan PFL-like (CL0339), which has the following description:

The N- and C-terminal halves of the structure have similar topologies but in some cases only one is represented by the members here, viz; the C-terminal domain of the R1 subunit of ribonucleotide reductase, and the N-terminal of PFL. The full-length structure is modelled by NRDD.

The clan contains the following 6 members:

DUF3029 DUF711 Gly_radical NRDD PFL-like Ribonuc_red_lgC

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(78)
Full
(4727)
Representative proteomes UniProt
(21570)
NCBI
(29888)
Meta
(10257)
RP15
(1443)
RP35
(3577)
RP55
(6162)
RP75
(9549)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

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  Seed
(78)
Full
(4727)
Representative proteomes UniProt
(21570)
NCBI
(29888)
Meta
(10257)
RP15
(1443)
RP35
(3577)
RP55
(6162)
RP75
(9549)
Alignment:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(78)
Full
(4727)
Representative proteomes UniProt
(21570)
NCBI
(29888)
Meta
(10257)
RP15
(1443)
RP35
(3577)
RP55
(6162)
RP75
(9549)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Prosite
Previous IDs: ribonuc_red_lgC;
Type: Family
Author: Finn RD, Griffiths-Jones SR
Number in seed: 78
Number in full: 4727
Average length of the domain: 431.50 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 63.16 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 19.5 19.5
Trusted cut-off 19.5 20.1
Noise cut-off 19.2 19.4
Model length: 524
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

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Interactions

There are 7 interactions for this family. More...

ATP-cone Ribonuc_red_lgC Ribonuc_red_lgN Ribonuc_red_lgN RNR_N LAGLIDADG_3 Ribonuc_red_sm

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Ribonuc_red_lgC domain has been found. There are 152 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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